Pavel visits the lab of Prof. Tatjana Sauka-Spengler in Oxford

In mid-March 2016, Pavel visited the lab of our collaborator Prof. Tatjana Sauka-Spengler in Oxford, UK. Tatjana’s lab established a genetically encoded system for biotinylation of specific targets in fish cells, allowing, among other applications, tissue-specific isolation of nuclei.

Supervised by a cheerfully enthusiastic PhD student Vanessa Chong, Pavel performed several rounds of nuclei isolation and is looking forward to introduce this method to Vastenhouw lab. 

Apart from having great time in Tatjana’s lab, Pavel also explored the charming campus of the Oxford University.

Thanks the entire Sauka-Spengler lab for a great time!

Setting up the experiment

Segmented Cells

FISHing fish, explained on thenode

Our recent publication is covered in a piece on FISHing fish. Check out the description and a bit of a behind-the-scenes insight into of the paper!

Link to post on thenode

Paper reference:

Stapel, L Carine; Lombardot, Benoit; Broaddus, Coleman; Kainmueller, Dagmar; Jug, Florian; Myers, Eugene W.; Vastenhouw, Nadine L.
Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos
Development, 143, no. 3, pp. 540-546, (2016)

Methods Article in ‘Development’

We are happy to post about our lab’s recent publication in Development. The article describes how to label and analyze single mRNA molecules, within single cells, at different stages of the zebrafish embryo’s development. With this technique, we hope to open new avenues into gene expression patterns and cellular differentiation programs.

The project was chiefly driven Carine Stapel, currently a PhD student in the Vastenhouw Lab. Carine developed the experimental protocol. The associated, freely available image analysis and quantification pipeline was developed in collaboration with Gene Myer’s research group as well as the Scientific Computing Facility. In fact, all work was done in-house at the MPI-CBG, demonstrating the institute’s wide array of qualifications as well as its collaborative spirit.

The article and protocol are available from Development, and the article also contains the analysis pipeline in its Supplementary Information. Article Page at Development

Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos

L. Carine StapelBenoit LombardotColeman BroaddusDagmar KainmuellerFlorian JugEugene W. MyersNadine L. Vastenhouw; 
Yuko, Lennart, and LZ1

Short Visit from Yuko Sato

Our collaborator Yuko Sato paid us a short visit from Japan. Yuko is a Kimura Lab Members at the Tokyo Institute of Technology, who develop innovative in vivo imaging approaches targeting post-translational modifications.

During the visit, Yuko and Lennart executed pilot experiments for light sheet-based in vivo imaging. We hope the photo conveys our joy at the last, successful attempt at our experiments. Thank you for the visit!

Mykola Markadeiev

Mykola was born in Ukraine and has a passion for trekking, skydiving and (suddenly) table-tennis. He studied Molecular Biology and Genetics in Taras Shevchenko University of Kyiv, where he took part in projects on liver regeneration and gerontology. Willing to explore Europe, the spirit of scientific adventure brought him to Dresden, doing his Masters in Regenerative Biology and Medicine. There he participated in research on murine neurogenesis, zebrafish regeneration and stem cell niches of Drosophila. He joined the Vastenhouw lab to help the project of Carine Stapel on single molecule RNA imaging.

Lucia Selfa

Lucia was born in Madrid and started her studies in Biomedical Sciences in Alcalá de Henares. By the end of her degree, her interest to discover the world dragged her to join the Erasmus program and move to Amsterdam, where she had her first contact with epigenetics during her Bachelor Thesis at the Netherlands Cancer Institute, participating in a haploid genetic screen of inhibitors targeting epigenetic modifiers.  Willing to explore other fields in science, as well as other countries and cultures, she joined the Master’s Program in Regenerative Biology and Medicine in Dresden. After looking into adult neurogenesis and planarian regeneration, she has now joined the lab to help understanding the role of histones in transcriptional regulation.